[methods in molecular biology] mobile genetic elements volume 859 || using and understanding repeatmaskerBigot, Yves
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low-complexity DNA sequences. In this chapter, we present the procedure to routinely use this program on a personal computer.This is a preview of subscription content, log in via an institution to check access. Si...
Chapter 2 Using and Understanding RepeatMasker Sébastien Tempel Abstract RepeatMasker is a program that screens DNA sequences for interspersed repeats and low-complexity DNA sequences. In this chapter, we present the procedure to routinely use this program on a personal computer. Key words: Repeats,...
Tempel S. Using and understanding repeatMasker. Methods Mol Biol. 2012;859:29–51. Article CAS Google Scholar Wheeler TJ, Eddy SR. Nhmmer: DNA homology search with profile HMMs. Bioinformatics. 2013;29:2487–9. Article CAS Google Scholar Pugacheva V, Korotkov A, Korotkov E. Search of...
Subsequently, a comprehensive library was constructed by merging sequences from Dfam v3.627 and Repbase28 with those identified by RepeatModeler. With this enriched library as a reference, we utilized RepeatMasker v4.1.329 to detect the repetitive sequences throughout the genome. This approach led ...
sites. Assessing polyclonality vs monoclonality of metastatic seeding is crucial for a correct understanding of the metastatic cascade, especially when accumulating evidence from patient samples and the model system paints a complex and often discordant picture of a mixture of both monoclonal and polyc...
Prior to gene prediction, potential transposable elements (TE) were identified using RepeatModeler (v2.0.3), a de novo transposable element identification and modeling package. Using default parameters, a database of TE families was built. Next, RepeatMasker (v4.1.0) was used to softmask the ge...
[3]. There are also large inversions and other structural variations that contribute to fitness [4,5] and significant variation in genome size caused by tandem repeat arrays [6]. Understanding this remarkable structural diversity is important for the continued improvement of maize, but the high ...
The completeness of the assem- blies based on CLR and HiFi reads was evaluated using BUSCO (BUSCO version 4.0.6; busco -m genome -l nematoda_odb10) [45, 46], and the length of repeti- tive elements was estimated based on repeat-masked genomic sequences using RepeatMasker (...
(>50 bp) called from a haplotype-resolved assembly23. Using RepeatMasker24, we selected insertions annotated as L1, Alu or SVA sequences, and identified high-confidence TE insertions by manually confirming that each insertion had a polyA tail and target-site duplication/deletion using the IGV...